The different phases of α-, β-, and γ-graphyne, which are new types of two-dimensional carbon allotropes, hold promise as potential candidates for designing substrate discs in piezoelectric nanogenerators. Accurate modeling of the bending rigidity and stretching properties as well as resonance frequencies of these materials is crucial for engineering applications like nano-resonator and nanogenerator systems. This step is imperative in designing and advancing future applications involving these structures. This study aims to create a hybrid atomistic-continuum model for modeling graphyne monolayers used as substrate discs in nanogenerators. The model integrates the benefits of both atomistic and continuum approaches. Based on the results, α-graphyne is the least mechanically stable, while γ-graphyne is the most stable. However, in terms of vibration frequency, α-graphyne has the highest frequency while γ-graphyne has the lowest. Therefore, β-graphyne, with moderate stability and resonance frequency, is recommended as the ideal choice for the substrate disc in piezoelectric nanogenerators. It can function within the Q-F frequency range (30–140 GHz) and induce deformation in the piezoelectric shim as well as generation voltage.